Dr. Shanmukhappa was research fellow in Division of Gastroenterology, Hepatology and Nutrition from 2003 to 2009 where he primarily worked on understanding the molecular mechanism involved in liver repair and regeneration as well as the induction of pancreatic cells in liver during defective liver repair. He identified the role of plasmin in liver repair. He has shown that plasmin mediates liver repair through the activation of HGF-MET signaling mainly affecting cell motility.

Dr. Shanmukhappa has an active research career with his primary interests in molecular control of liver repair, regeneration, biliary atresia, NASH and metabolic complications of HIV.